As I understand it, the issue is not in the failure rate of optical scanning, but in the proposed process to scan them in a centralized location, rather than scanning them at the polling location as the voter submits their ballot.

If the machine rejects the ballot as the voter submits it, they have a chance to correct any errors or issues related to their submission. If the machine rejects the ballot later in the day, they have no such opportunity.

The ACLU, in this case, seems to just be trying to make sure every ballot is actually counted.